Biophysical Chemistry

Biophysical Chemistry, Volume I: Thermodynamics, Electrostatics, and the Biological Significance of the Properties of Matter focuses on the biological aspects of the properties of matter, putting emphasis on the chemical elements, water and carbon dioxide, complex molecules, and proteins.

The publication first elaborates on biochemistry and geochemistry, water and its biological significance, and the problems of protein structure. Discussions focus on the number of peptide chains in the molecule and nature of terminal groups, latent heat of fusion, characteristics of the amino acids derived from proteins, expansion of water in freezing, and the relative abundance of chemical elements in the universe. The text then takes a look at thermodynamics and the application to polar molecules and ionic solutions of electrostatics, including free energy of a charged sphere, image charges, salting-out effect, expressions for the change of fundamental thermodynamic functions, and chemical potentials.

The book examines the conductivity of electrolytes, acid-base equilibria, and polybasic acids, bases, and ampholytes, including proteins. Topics include ionization of cysteine, isoelectric points of polyvalent ampholytes, hemoglobin, nature of acids and bases, measurement of conductivity, electrolytes as conductors, and the moving boundary method of determining transference numbers.

The manuscript is a dependable reference for chemists and researchers interested in thermodynamics, electrostatics, and the biological value of the properties of matter.

Preface

Symbols

1. Biochemistry and Geochemistry

Distribution of the Chemical Elements in Living Organisms

The Relative Abundance of the Chemical Elements in the Universe

The Structure of the Earth and Its Crust

Early History of the Earth

The Ocean

The Central Role of Carbon in Biology

References

2. Water and Its Biological Significance

Heat Capacity of Water and Other Substances

Heat of Vaporization

Latent Heat of Fusion

The Expansion of Water in Freezing

Surface Tension

Dielectric Constant of Water

Solubility

References

3. Problems of Protein Structure

Proteins; Some General Considerations

Amino Acids and Peptides as Dipolar Ions

Characteristics of the Amino Acids Derived from Proteins

Amino Acid Analysis of Proteins

Polypeptide Chains and Their Presence in Proteins

Determination of Arrangement of Peptide Chains and Their Linkage within Protein Molecules

The Number of Peptide Chains in the Molecule, and the Nature of the Terminal Groups

Cross-Linkages Between Peptide Chains: Disulfide and Phosphate Cross-Linkages

Phosphate Cross-Linkages

Other Cross-Linkages

Sequence of Amino Acid Residues in Peptide Chains

Disulfide Linkages in Insulin and Ribonuclease

Spatial Configurations of Polypeptide Chains

Silk Fibroin

β-Keratin

α-Keratin and Synthetic Polypeptides: the α-Helix and Other Possible Helical Structures

Collagen

Amino Acid Composition

Heat Shrinkage

The Structural Pattern—Evidence from X-Ray and Electron Microscope Studies

Collagen Structure

The Stability of Helical Structures

The Significance of Disulfide Bonds; Cross-Linkages and Loops in Peptide Chains

Possible Stereochemistry of Insulin

Stereochemistry and Enzyme Activity of Ribonuclease

Helical and Nonhelical Regions in Globular Proteins

References

4. Thermodynamics

Introduction

Systems and Phases

Temperature

Dimensions of Temperature

First Law

Second Law

Irreversible Processes

Maximum Work, Equilibrium, and Free Energy

Heat Content, or Enthalpy

Expressions for the Change of the Fundamental Thermodynamic Functions

Partial Molal Quantities

Chemical Potentials

Phase Rule

Activities

Ideal or Perfect Solutions and Raoult's Law

Activity Coefficients and the Choice of Standard States

Activity and Chemical Potential of a Nonvolatile Solute from the Vapor Pressure of the Solvent

Equilibrium Between Phases; Activities in Relation to Distribution Coefficients and Solubilities

Activity of Strong Electrolytes

Mass Law

The Malate-Fumarate Equilibrium

Peptide Bond Synthesis in the Reaction Between Benzoyl-L-Tyrosine and Glycinamide

The Standard Free Energy of Hydrolysis of Adenosine Triphosphate

Systems Involving Other Variables

Elastic Bodies

Systems in Gravitational or Centrifugal Fields

Statistical Interpretation of Entropy

Entropy of a Perfect Crystal at 0°K

Entropy Change on Mixing of Components in an Ideal Solution

The Residual Entropy of Ice

Standard Free Energies of Formation and Their Use in Determining Thermodynamic Equilibria

The Fumarate-Malate Equilibrium

The First Ionization of Carbonic Acid

Standard Free Energy of Peptide Bond Synthesis

References

5. Electrostatics: Its Application to Polar Molecules and Ionic Solutions

Definition of the Potential

Gauss's Law

Poisson's Equation for Regions Containing a Space Charge

Free Energy of a Charged Sphere

The Potential and Energy of a Dipole

Image Charges

The Salting-Out Effect

Salting Out of Proteins

Effects of Dipolar Ions

Debye's Theory of Salting Out by Redistribution of Solvent Molecules Around the Ions

Ionic Interactions and the Debye-Hückel Theory

Ion-Dipole Interactions

Experimental Studies on the Solubility of Dipolar Ions, and Their Interaction with Ions

Solubilities and Activity Coefficients in Water and Other Media

Solubilities in the Presence of Salt

References

6. Dielectric Constants and Their Significance

Introduction to Dielectric Constants and Dipole Moments

Dielectric Polarization in Relation t o Molecular Properties

The Debye Theory of the Dielectric Constant

Application of the Debye Theory

The Breakdown of the Debye Theory in Polar Liquids

Modifications of the Debye Theory

The Onsager Theory

Kirkwood's Theory

Polar Liquids and Dipolar Ions

Dielectric Constants and Dipole Moments of Dipolar Ions in Solution

Methods of Measuring Dielectric Constant

References

7. Conductivity of Electrolytes

Conductance and Resistance

Electrolytes as Conductors

Faraday's Law

Equivalent Conductivity

Ion Mobilities

Ion Conductances

Transference Numbers

Hittorf Method of Determining Transference Numbers

The Moving Boundary Method of Determining Transference Numbers

Theoretical Considerations Regarding Equivalent Conductance; Effects of Interionic Forces

Measurement of Conductivity

References

8. Acid-Base Equilibria

The Nature of Acids and Bases

The Concept of pH; a Preliminary Statement

Calculations of pH in Systems of Acids of Known Acid Strengths

The Titration of a Weak Acid with a Strong Base; Buffer Action

The Experimental Determination of Acidity Constants (KA Values)

The Conductivity Method

The Indicator Method for Determining Relative Strengths of Acids

Electromotive Force Measurements and pH Determination

Standard Potentials of Half-Cells, Choice of Conventions

Evaluation of pKA from Cells without Liquid Junction

Cells Containing Liquid Junctions

The Liquid Junction Potential

Variation of pH with Ionic Strength for Acid-Base Pairs of Different Charge Types

Choice of a Standard for Calibrating pH Measurements

The Glass Electrode

Determination of pKA Values and Related Thermodynamic Functions in Relation to Structure

Effect of Neighboring Charged Groups and Dipoles on pKA Values

Other Acidic Groups of Biochemical Interest

Phenolic Hydroxyl Groups

Imidazole Groups

Sulfhydryl Groups

The Guanidinium Group

The Peptide Linkage

Purines, Pyrimidines, Nucleosides, and Nucleotides

Effects of Variation in Dielectric Constant of Solvent on Relative Strength of Acids of Different Charge Types

Problems

References

9. Polybasic Acids, Bases, and Ampholytes, Including Proteins

Dibasic Acids

Polyvalent Acids: General Relations

A Specific Case: Glutamic Acid

Spectroscopic Determination of Microscopic Constants: The Ionization of Cysteine

Isoelectric Points of Amphoteric Substances

Isoelectric Points of Polyvalent Ampholytes

Equilibrium Between Different Ionic Forms in Polyvalent Acids and Ampholytes: The Equation of Linderstrøm-Lang

Electrostatic Effects on Ionization in Polybasic Acids. The Charged Sphere Model

Formulation in Terms of Association Constants

Acid-Base Equilibria in β-Lactoglobulin Solutions

Ovalbumin

Serum Albumins

Ribonuclease

Hemoglobin

Other Proteins

Synthetic Polyelectrolytes, Including Polypeptides

Effects of Internal Hydrogen Bonding on Titration Curves

Calculations with a Dielectric Sphere Model Containing Fixed Charges

References

10. Carbon Dioxide and Carbonic Acid

Carbon Dioxide in Nature

Structural Considerations

The Fundamental Equilibria in Systems Containing Carbon Dioxide and Carbonic Acid

Absorption Coefficients of Carbon Dioxide in Water

The Reversible Hydration of Carbon Dioxide and the Ionization of Carbonic Acid

Carbon Dioxide Dissociation Curves

The Formation of Carbamates

Rates of the Reactions CO2 + H2O → H2CO3

The Velocity of the Dehydration Reaction: H2CO3 → H2O + CO2

The Hydration Reaction: CO2 + H2O → H2CO3

Carbonic Anhydrase

References

11. Some General Aspects of Molecular Interactions

Some Methods of Measuring Binding

Equilibrium Dialysis

Ultrafiltration

Spectroscopic Measurements

Electromotive Force Measurements

Ultracentrifuge Measurements

Electrophoresis

Effects of pH Changes When Salts Are Added: Isoionic Points

Isoelectric and Isoionic Solutions

Some Fundamental Considerations Regarding Certain Types of Binding

Interactions of Bound Groups

Competition Effects

Interactions Between Different Kinds of Bound Groups

Formation of Chelate Complexes

Binding by a Set of Equivalent and Independent Groups

The Logarithmic Plot: Bjerrum's "Formation Function"

The Reciprocal Plot

The Scatchard Plot of v/(A) against v

Relation of Equations for Binding to Those of Enzyme Kinetics

General Equation for Binding by a Molecule or Ion with n Sites Available for Combination

Binding by an Equivalent Set of Groups with Interactions Between Them

Complexes of Biochemical Substances with Metallic Ions: Some General Considerations

Electrostatic Effects on Binding of Ions

Effects of Competition Between Different Ligands for the Same Binding Site

Linked Functions

References